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1,876 results for “pathology”
Fig. 7 in Pathological phalanges in a camarasaurid sauropod dinosaur and implications on behaviour
Fig. 7. Smoothened area (a possible case of eburnation) on the distal articular surface of the left manual phalanx I-1 of the camarasaurid sauropod SMA 0002 from Upper Jurassic Morrison Formation, Howe-Stephens Quarry, Wyoming, USA. The distal dorsopalmar height is 55 mm.
Fig. 6. Overgrowth type 2 in Pathological phalanges in a camarasaurid sauropod dinosaur and implications on behaviour
Fig. 6. Overgrowth type 2 exemplified in a drawing (A, modified from Tschopp et al. 2015) and CT scan (B) of the left manual phalanx II-1 of the camarasaurid sauropod SMA 0002 from Upper Jurassic Morrison Formation, Howe-Stephens Quarry, Wyoming, USA. CT scan shows variable bone densities in the osteophyte, indicated by the different gray scales. Abbreviations: phm, phalanx of manual digit; mc, metacarpal.
Fig. 5 in Pathological phalanges in a camarasaurid sauropod dinosaur and implications on behaviour
Fig. 5. Thin section of the overgrowth type 1 from the right pedal ungual I of the camarasaurid sauropod SMA 0002 from Upper Jurassic Morrison Formation, Howe-Stephens Quarry, Wyoming, USA (A). Detail (B), showing coarse-grained structure bone in mainly avascular bone (arrowheads).
Fig. 4 in Molecular characterization of the re-emerging West Nile virus in avian species and equids in Israel, 2018, and pathological description of the disease
Fig. 4 Replication of yellow-legged seagull-derived WNV in Vero and C6/36 cells. Cytopathic effect (left) was observed after one passage in both cell lines. The control cells (right) were grown under the same conditions. Scale-bars: 100 µM
Fig. 5 in Molecular characterization of the re-emerging West Nile virus in avian species and equids in Israel, 2018, and pathological description of the disease
Fig. 5 Phylogenetic analysis of West Nile viruses (WNVs) from avian and equine hosts studied in Israel during 2016 and 2018. The analysis was conducted on a nucleotide sequence of the genes encoding the capsid, pre-membrane protein, and membrane protein, using the neighbor-joining method implemented in MEGA X software. The robustness of branching pattern was tested by 1000 bootstrap replications. The rates among sites algorithm used was gamma distribution with invariant sites (G+I). The bar denotes 0.02 nucleotide substitutions per site. Lineage 1 and 2 reference strains are present with country and year of isolation. The GenBank annotated sequences are underlined and the sequences obtained in this study (during 2016 and 2018) are marked with rectangles
Spatial Tumor-Immune Analysis: Insights from Pathology Slides and Breast Cancer Survival
<p>Cancer is the second leading cause of death in the US. Among the various forms of cancer, breast cancer and lung cancer are particularly significant due to their prevalence and impact. Breast cancer in particular contributing to around 30\% of all new female cases each year, while also having some of the highest mortality rates. Scientists and doctors rely on pathology slides to aid in the discovery of a cure, diagnose patients, and provide treatment. These slides play a crucial role in examining samples and identifying any abnormalities. The primary goal of this project was to analyze pathology slides from 873 cancer patients in The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA). We developed STAIN (Spatial Tumor and Immune Analysis for Novel insights) with the hypothesize that quantitative analysis of cell type specific clusters in the spatial context can lead to novel insights on patient survival. First, we identified tumor and immune cells using a HD-Yolo algorithm. Then we identify tumor clusters and immune cell clusters. Next, descriptive statistics such as Jaccard distance, Hausdorff distance, Wasserstein distance, tumor density, and immune cell density were derived and correlated with the patients survival while adjusting for clinical attributes such as patient age and tumor stage using Cox proportional Hazard models. The results discover spatial attributes and known clinical risk features associated with survival. </p>
Linked collectors and determiners for: New South Wales Plant Pathology and Mycology Herbarium (DAR) AVH data.
Natural history specimen data linked to collectors and determiners held within, "New South Wales Plant Pathology and Mycology Herbarium (DAR) AVH data". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/685cff6d-e439-4552-980c-5c73d647d1bf">https://bionomia.net/dataset/685cff6d-e439-4552-980c-5c73d647d1bf</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/685cff6d-e439-4552-980c-5c73d647d1bf">https://gbif.org/dataset/685cff6d-e439-4552-980c-5c73d647d1bf</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Records of the DAFWA Plant Pathology Collection.
Natural history specimen data linked to collectors and determiners held within, "Records of the DAFWA Plant Pathology Collection". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/3d93e795-10d9-41fd-8eca-579c2aca513e">https://bionomia.net/dataset/3d93e795-10d9-41fd-8eca-579c2aca513e</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/3d93e795-10d9-41fd-8eca-579c2aca513e">https://gbif.org/dataset/3d93e795-10d9-41fd-8eca-579c2aca513e</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Cornell University Plant Pathology Herbarium.
Natural history specimen data linked to collectors and determiners held within, "Cornell University Plant Pathology Herbarium". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/8e7562e2-a8ce-4b80-bad9-d7f115534865">https://bionomia.net/dataset/8e7562e2-a8ce-4b80-bad9-d7f115534865</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/8e7562e2-a8ce-4b80-bad9-d7f115534865">https://gbif.org/dataset/8e7562e2-a8ce-4b80-bad9-d7f115534865</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Cornell University Plant Pathology Herbarium.
Natural history specimen data linked to collectors and determiners held within, "Cornell University Plant Pathology Herbarium". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/5a6538b8-e35c-46c4-8978-6858a657a75f">https://bionomia.net/dataset/5a6538b8-e35c-46c4-8978-6858a657a75f</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/5a6538b8-e35c-46c4-8978-6858a657a75f">https://gbif.org/dataset/5a6538b8-e35c-46c4-8978-6858a657a75f</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Records of the Queensland Plant Pathology Herbarium.
Natural history specimen data linked to collectors and determiners held within, "Records of the Queensland Plant Pathology Herbarium". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/5d11316c-4237-41cc-aba0-1288b532d5c2">https://bionomia.net/dataset/5d11316c-4237-41cc-aba0-1288b532d5c2</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/5d11316c-4237-41cc-aba0-1288b532d5c2">https://gbif.org/dataset/5d11316c-4237-41cc-aba0-1288b532d5c2</a>. Formatted as a Frictionless Data package.
Fig. 86. Prionocyclus wyomingensis Meek, 1876. Pathological specimen lacking keel. USNM 475903 in A Revision Of The Turonian Members Of The Ammonite Subfamily Collignoniceratinae From The United States Western Interior And Gulf Coast
Fig. 86. Prionocyclus wyomingensis Meek, 1876. Pathological specimen lacking keel. USNM 475903, ex J.I. Kirkland Collection, from the Juana Lopez Member of the Mancos Shale, in the SE1/4 sec. 4, T. 12S, R. 1E, Garfield County, Colorado. Figures are X1.
Single-synapse analyses of Alzheimer's disease implicate pathologic tau, DJ1, CD47, and ApoE
<p>Synaptic molecular characterization is limited for Alzheimer's disease (AD). Our newly invented mass cytometry-based method, Synaptometry by Time of Flight (SynTOF), was used to measure 38 antibody probes in approximately 17 million single-synapse events from human brains without pathologic change or with pure AD or Lewy body disease (LBD), non-human primates (NHP), and PS/APP mice. Synaptic molecular integrity in humans and NHP was similar. Although not detected in human synapses, Aβ was in PS/APP mice single-synapse events. Clustering and pattern identification of human synapses showed expected disease-specific differences, like increased hippocampal pathologic tau in AD and reduced caudate dopamine transporter in LBD, and revealed novel findings including increased hippocampal CD47 and lowered DJ1 in AD and higher ApoE in AD with dementia. Our results were independently supported by multiplex ion beam imaging of intact tissue. This highlights the higher depth and breadth of insight on neurodegenerative diseases obtainable through SynTOF.</p>
Raman spectra of urine from patients with diabetes mellitus and other pathologies
<p>This dataset contains raw (<strong>unprocessed Raman spectra</strong>) of urine from de-identified human patients. Analysis of this dataset is included in our journal article, "<em><strong>Analysis of urine Raman spectra differences from patients with diabetes mellitus and other pathologies</strong></em>." The dataset includes urine Raman spectra from (1) healthy volunteers, (2) patients with chronic kidney disease and diabetes mellitus, (3) patients with chronic kidney disease and without diabetes mellitus, (4) patients with biopsy-confirmed diabetic nephropathy, (5) patients with biopsy-confirmed immune-mediated nephropathy, (5) patients with biopsy-confirmed membranous nephropathy, (6) patients with biopsy-confirmed renal neoplasm, (7) patients with other glomerular pathologies, and (8) Surine (urinalysis control).</p> <p>Raman spectra were obtained with the following parameters:</p> <ul> <li>Raman spectrometer: Agiltron PeakSeeker PRO-785</li> <li>Mode: Bulk liquid scanning</li> <li>Wavelength: 785 nm</li> <li>Wavenumber range: 200-2000 cm-1</li> <li>Laser power: 30 mW</li> <li>Spectral resolution: 8 cm-1</li> <li>Laser spot size: 0.2 mm</li> <li>Excitation time: 30 s</li> </ul> <p>Raman spectral data and de-identified metadata are present in tab-separated value (tsv) files. Each urine sample is bar-code identified and linked to a disease state (or control) in the metadata tsv file. Ten (10) independent Raman scan replicates exist for each urine sample and are identified by bar-code in the spectral data tsv file. The study IRB approval and a sample blank patient consent form are also included here.</p>
Metastability as a neuromechanistic biomarker of schizophrenia pathology
<p>Matlab files for Human Connectome Project - Early Psychosis (HCPEP) and COBRE in AAL116 parcellation.</p> <p>HCPEP files contain data for 4 runs of resting-state fMRI for healthy controls and non-affective psychosis groups.</p> <p>COBRE files contain data for 1 run of resting-state fMRI for healthy controls and established schizophrenia groups.</p>
Synaptic oligomeric tau in Alzheimer's disease – a potential culprit in the spread of tau pathology through the brain
<p>In Alzheimer’s disease (AD), fibrillar tau pathology accumulates and spreads through the brain and synapses are lost. Evidence from mouse models indicates that tau spreads trans-synaptically from pre- to postsynapses and that oligomeric tau is synaptotoxic, but data on synaptic tau in human brain is scarce. Here we used sub-diffraction-limit microscopy to study synaptic tau accumulation in post-mortem temporal and occipital cortices of human AD and control donors. Oligomeric tau is present in both pre- and postsynaptic terminals even in areas without abundant fibrillar tau deposition. Further, there is a higher proportion of oligomeric tau compared to phosphorylated or misfolded tau found at synaptic terminals. These data suggest that accumulation of oligomeric tau in synapses is an early event in disease pathogenesis, and that tau pathology may progress through the brain via trans-synaptic spread in human disease. Thus, specifically reducing oligomeric tau at synapses may be a promising therapeutic strategy for AD.</p>
MedalCare-XL: 16,900 healthy and pathological synthetic 12 lead ECGs obtained through electrophysiological simulations
<p>Mechanistic cardiac electrophysiology models allow for personalized simulations of the electrical activity in the heart and the ensuing electrocardiogram (ECG) on the body surface. As such, synthetic signals possess precisely known ground truth labels of the underlying disease (model parameterization) and can be employed for validation of machine learning ECG analysis tools in addition to clinical signals. Recently, synthetic ECG signals were used to enrich sparse clinical data for machine learning or even replace them completely during training leading to good performance on real-world clinical test data.<br> <br> We thus generated a large synthetic database comprising a total of 16,900 12 lead ECGs based on multi-scale electrophysiological simulations equally distributed into 1 normal healthy control and 7 pathology classes. The pathological case of myocardial infraction had 6 sub-classes. A comparison of extracted timing and amplitude features between the virtual cohort and a large publicly available clinical ECG database demonstrated that the synthetic signals represent clinical ECGs for healthy and pathological subpopulations with high fidelity. The novel dataset of simulated ECG signals is split into training, validation and test data folds for development of novel machine learning algorithms and their objective assessment. </p> <p>This folder WP2_largeDataset_Noise contains the 12 lead ECGs of 10 seconds length. Each ECG is stored in a separate CSV file with one row per lead (lead order: I, II, III, aVR, aVL, aVF, V1-V6) and one sample per column (sampling rate: 500Hz). Data are split by pathologies (avblock = AV block, lbbb = left bundle branch block, rbbb = right bundle branch block, sinus = normal sinus rhythm, lae = left atrial enlargement, fam = fibrotic atrial cardiomyopathy, iab = interatrial conduction block, mi = myocardial infarction). MI data are further split into subclasses depending on the occlusion site (LAD, LCX, RCA) and transmurality (0.3 or 1.0). Each pathology subclass contains training, validation and testing data (~ 70/15/15 split). Training, validation and testing datasets were defined according to the model with which QRST complexes were simulated, i.e., ECGs calculated with the same anatomical model but different electrophysiological parameters are only present in one of the test, validation and training datasets but never in multiple. Each subfolder also contains a "siginfo.csv" file specifying the respective simulation run for the P wave and the QRST segment that was used to synthesize the 10 second ECG segment. Each signal is available in three variations:</p> <ul> <li>*_raw.csv contains the synthesized ECG without added noise and without filtering</li> <li>*_noise.csv contains the synthesized ECG (unfiltered) with superimposed noise</li> <li>*_filtered.csv contains the filtered synthesized ECG (fiter settings: highpass cutoff frequency 0.5Hz, lowpass cutoff frequency 150Hz, butterworth filters of order 3).</li> </ul> <p>The folder WP2_largeDataset_ParameterFiles contains the parameter files used to simulate the 12 lead ECGs. Parameters are split for atrial and ventricular simulations, which were run independently from one another. <br> See <a href="https://doi.org/10.48550/arXiv.2211.15997">Gillette*, Gsell*, Nagel* et al. "MedalCare-XL: 16,900 healthy and pathological synthetic 12 lead ECGs obtained through electrophysiological simulations"</a> for a description of the model parameters.</p>
Evolutionary gain and loss of a pathological immune response to parasitism
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Data from: Open-top Bessel beam two-photon light sheet microscopy for three-dimensional pathology
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Single-synapse analyses of Alzheimer’s disease implicate pathologic tau, DJ1, CD47, and ApoE
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.